Calculate Pairwise Distance from a Matrix

Calculate Pairwise Distance from a Matrix

dist2(x, pairwise_fun = function(x, y) sqrt(sum((x - y)^2)), ...)

Arguments

x	A matrix or a list. If it is a matrix, the distance is calculated by rows.
pairwise_fun	A function which calculates distance between two vectors.
...	Pass to as.dist.

Details

You can construct any type of distance measurements by defining a pair-wise distance function. The function is implemented by two nested for loops, so the efficiency may not be so good.

Value

A dist object.

Examples

lt = lapply(1:10, function(i) {
    sample(letters, sample(6:10, 1))
})
dist2(lt, function(x, y) {
    length(intersect(x, y))/length(union(x, y))
})
#>             1          2          3          4          5          6          7
#> 2  0.26666667                                                                  
#> 3  0.15384615 0.14285714                                                       
#> 4  0.12500000 0.26666667 0.25000000                                            
#> 5  0.14285714 0.41666667 0.08333333 0.33333333                                 
#> 6  0.20000000 0.35714286 0.07142857 0.20000000 0.45454545                      
#> 7  0.38461538 0.26666667 0.07142857 0.28571429 0.14285714 0.12500000           
#> 8  0.20000000 0.18750000 0.15384615 0.12500000 0.06666667 0.20000000 0.20000000
#> 9  0.05882353 0.18750000 0.15384615 0.28571429 0.33333333 0.12500000 0.05882353
#> 10 0.28571429 0.26666667 0.15384615 0.28571429 0.14285714 0.12500000 0.28571429
#>             8          9
#> 2                       
#> 3                       
#> 4                       
#> 5                       
#> 6                       
#> 7                       
#> 8                       
#> 9  0.12500000           
#> 10 0.12500000 0.28571429